ENH: add new type called FeatureTable[Unconstrained] (#386)

Author: VinzentRisch

q2_types/feature_table/__init__.py

@@ -10,9 +10,9 @@
                        BIOMV210DirFmt)
 from ._types import (FeatureTable, Frequency, RelativeFrequency,
                      PresenceAbsence, Composition, Balance,
-                     PercentileNormalized, Design, Normalized)
+                     PercentileNormalized, Design, Normalized, Unconstrained)
 
 __all__ = ['BIOMV100Format', 'BIOMV100DirFmt', 'FeatureTable', 'Frequency',
            'RelativeFrequency', 'PresenceAbsence', 'BIOMV210Format',
            'BIOMV210DirFmt', 'Composition', 'Balance', 'PercentileNormalized',
-           'Design', 'Normalized']
+           'Design', 'Normalized', 'Unconstrained']

q2_types/feature_table/_deferred_setup/__init__.py

@@ -15,7 +15,7 @@
 from .. import (BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
                 BIOMV210DirFmt, FeatureTable, Frequency, RelativeFrequency,
                 PresenceAbsence, Composition, Balance,
-                PercentileNormalized, Design, Normalized)
+                PercentileNormalized, Design, Normalized, Unconstrained)
 
 from ...plugin_setup import plugin
 
@@ -27,7 +27,8 @@
 
 plugin.register_semantic_types(FeatureTable, Frequency, RelativeFrequency,
                                PresenceAbsence, Balance, Composition,
-                               PercentileNormalized, Design, Normalized)
+                               PercentileNormalized, Design, Normalized,
+                               Unconstrained)
 
 plugin.register_artifact_class(
     FeatureTable[Frequency],
@@ -81,5 +82,11 @@
     directory_format=BIOMV210DirFmt,
     description="A feature table that was normalized."
 )
-
+plugin.register_artifact_class(
+    FeatureTable[Unconstrained],
+    directory_format=BIOMV210DirFmt,
+    description="A feature table containing real-valued feature "
+                "measurements represented in Euclidean space without "
+                "constant-sum (compositional) constraints."
+)
 importlib.import_module('._transformers', __name__)

q2_types/feature_table/_types.py

@@ -34,3 +34,6 @@
 
 Normalized = SemanticType('Normalized',
                           variant_of=FeatureTable.field['content'])
+
+Unconstrained = SemanticType('Unconstrained',
+                             variant_of=FeatureTable.field['content'])

q2_types/feature_table/tests/test_types.py

@@ -14,7 +14,7 @@
                                     RelativeFrequency, PercentileNormalized,
                                     Composition, Balance,
                                     PresenceAbsence, BIOMV210DirFmt, Design,
-                                    Normalized)
+                                    Normalized, Unconstrained)
 
 
 class TestTypes(TestPluginBase):
@@ -41,6 +41,9 @@ def test_balance_semantic_type_registration(self):
     def test_normalized_semantic_type_registration(self):
         self.assertRegisteredSemanticType(Normalized)
 
+    def test_unconstrained_semantic_type_registration(self):
+        self.assertRegisteredSemanticType(Unconstrained)
+
     def test_feature_table_semantic_type_to_v210_format_registration(self):
         self.assertSemanticTypeRegisteredToFormat(
             FeatureTable[Frequency],
@@ -66,6 +69,9 @@ def test_feature_table_semantic_type_to_v210_format_registration(self):
         self.assertSemanticTypeRegisteredToFormat(
             FeatureTable[Normalized],
             BIOMV210DirFmt)
+        self.assertSemanticTypeRegisteredToFormat(
+            FeatureTable[Unconstrained],
+            BIOMV210DirFmt)
 
 
 if __name__ == "__main__":